rs9557207

Variant names:

• chr13-99384164-A-G
• rs9557207
• NM_001144072.2:c.928-1064A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001144072.2(UBAC2):​c.928-1064A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,176 control chromosomes in the GnomAD database, including 2,408 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.17 (2408 hom., cov: 33)
• Consequence: UBAC2 NM_001144072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46

Genes affected

UBAC2 (HGNC:20486): (UBA domain containing 2) Involved in negative regulation of canonical Wnt signaling pathway and negative regulation of retrograde protein transport, ER to cytosol. Acts upstream of or within protein localization to endoplasmic reticulum. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBAC2	NM_001144072.2	c.928-1064A>G		intron_variant	Intron 8 of 8	ENST00000403766.8	NP_001137544.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBAC2	ENST00000403766.8	c.928-1064A>G		intron_variant	Intron 8 of 8	2	NM_001144072.2	ENSP00000383911.3

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25772 AN: 152058 Hom.: 2406 Cov.: 33

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0558

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.205

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.169 AC: 25771 AN: 152176 Hom.: 2408 Cov.: 33 AF XY: 0.164 AC XY: 12237 AN XY: 74390

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.0560

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.203

Alfa AF: 0.215 Hom.: 3461

Bravo AF: 0.174

Asia WGS AF: 0.0720 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.13
DANN	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9557207; hg19: chr13-100036418;